A greedy collector, Lawrence III, wants to capture the legendary Pokemon, Lugia. But in order to do so, he must capture the Titans of Fire, Ice, and Lightning. The titans are powerful bird-like Pokemon, and if they are disturbed they will wage a war against eachother which will ultimately result in earth's destruction. Ash, Misty, and Tracey get caught up in the situation when they end up being washed ashore onto Shamouti Island. Soon after, Ash meets a girl named Melody who sends him into a mission where he must collect the 3 Orbs which will quell the fighting, but first Ash must gain help from the Beast of the Sea, Lugia, if he's to suceed.

A team of scientists use the DNA of a rare Pokemon, Mew, to create the world's strongest Pokemon, Mewtwo. Not wanting to be used as an experiment, Mewtwo uses its psychic powers in a violent rage to destroy the scientists who created it. Mewtwo then tries to learn how to focus his powers with the aid of Giovanni, the man who funded the scientists' operations, but discovers that it is being used again. So Mewtwo decides to find its own purpose in life, and carry out its revenge on humans by destroying life on earth by using a deadly storm. Ash Ketchum and a group of other Pokemon Trainers are summoned by Mewtwo to have a battle with it, but they soon discover that they're only being invited so Mewtwo can clone their Pokemon for it's own purposes. Ash then tries to find a way to stop Mewtwo's plot before it can be carried out.

Dr. Yung, an enigmatic Pokémon scientist, has developed a new Mirage system that uses computer data to resurrect extinct Pokémon, like Kabutops and Armaldo. Professor Oak, Ash and his companions show up at the Mirage Mansion at Dr. Yung's invitation, and watch a demonstration of the machine's capabilities. In the middle of a battle between Dr. Yung's Mirage Pokémon and Ash, the machine goes haywire and a Mirage Aerodactyl swoops in and kidnaps Dr. Yung. A man calling himself "The Mirage Master" appears and announces to everyone that the Mirage System can be used to create Pokémon with absolutely no weaknesses. Ash, Misty, and Professor Oak struggle to stop the madman and escape with their lives.

Satoshi and his friends get lost in an unknown wasteland. They eventually come across a "Water Pokemon Show" performed by the star of the Mariner Troupe, Hiromi. Hiromi is a descendant of the troupe of Water People able to communicate with water pokemon, and she tells our heroes the legend that's been passed down by her people for generations. According to legend, a temple the Water People built called "The Water Temple Akuusha" rests somewhere in the ocean, and a treasure called "The Water Crown" is hidden there. It's said that no one has ever seen this treasure, but that changes when a Pokemon Ranger named Jack Walker (aka Jackie) appears to chase aftert it. Jackie is on a top secret mission that has him protecting the egg of the leader of the water pokemon, Manaphy. This pokemon, called the "Prince of the Sea," needs to be taken to the Water Temple Akuusha, so Satoshi-tachi and Hiromi decide to help him. Along the way, a pirate named Phantom attacks our heroes from his great submarine. Phantom plans to use the Water Crown's power to help him conquer the world, but he'll have to solve the mystery of Manaphy's egg first. When the Rocket-Dan get into the mix, Jackie uses his Capture Styler to borrow the power of a nearby pokemon to stand up to them. Satoshi and Pikachu enter the fray, but they still have to contend with the attacks of Phantom's powerful high tech mecha! Suddenly, the egg starts to shine with a vivid light, and Manpahy is born! What is the mystery of the legendary treasure? What mysterious powers does Manaphy have? Can Satoshi-tachi and Jackie complete their top secret mission? The journey to reach the Water Temple Akuusha has begun!